Not sure if this is what they're using but there is VoxelJS[1] - it has a very healthy plugin ecosystem so you can get a functioning game up and running quite quickly.
VoxelJS is really cool, but not quite really suited to building something like Voxatron. You could however probably use straight ThreeJS, or go lib-less and roll your own WebGL system.
These games are all compiled from native languages to asm.js.
These games are all compiled from native languages to asm.js.